There are Win32 functions available that can disable and enable redirection.
[DllImport("kernel32.dll", SetLastError = true)]
static extern bool Wow64DisableWow64FsRedirection(ref IntPtr ptr);
[DllImport("kernel32.dll", SetLastError = true)]
static extern bool Wow64RevertWow64FsRedirection(IntPtr ptr);
Example:
IntPtr wow64Value = IntPtr.Zero;
// Disable redirection.
Wow64DisableWow64FsRedirection(ref wow64Value);
// Do whatever you need
// .....................
// Re-enable redirection.
Wow64RevertWow64FsRedirection(wow64Value);